Project properties

Title Identification of recessive alleles of candidate genes in potato
Group Plant Breeding, Laboratory of
Project type thesis
Credits 24-39
Supervisor(s) Herman van Eck and Corentin Clot
Examiner(s) Herman van Eck
Contact info herman.vaneck@wur.nl, corentin.clot@wur.nl
Begin date 2019/01/01
End date 2021/12/31
Description This projects aims to identify allelic variants of important genes in potato genomes. At Plant Breeding we have collected DNA sequence information of a large number of potato varieties. Bioinformatic analysis can identify alleles with deviating sequences, such as insertions, deletions, premature stop codons or affected splice sites. For several breeding traits (disease resistance, self-incompatibility, tuber shape, plant maturity, flesh colour) the underlying genes are known. However, we are hardly aware of the allelic variation for those genes, and the functional implications of such allelic variants. Neither do we know what alleles are represented in each potato variety.
Specific examples: (A) Diploid potato is self-incompatible, and this is controlled by the S-locus. This system is inactive in tetraploids, and without selection pressure we expect mutant S-alleles to arise. Diploid breeding requires such mutant S-alleles to allow inbreeding and repetitive back-crossing. A natural recessive allele is highly valuable, because alternatives (e.g. Crispr/Cas9) are considered as GMO products which cannot enter the market. (B) Diploids can be crossed with tetraploids if these diploids produce unreduced 2n gametes. Mutations in meiotic genes that abolish the first meiotic division are controlled by the ps locus, involved in parallel meiotic spindles. Identification of mutants are of great value to enable to switch from diploid to tetraploid potato breeding. (C) Cold storage of potatoes us applied to prevent sprouting, but tuber quality for French fries can be harmed. Cold-induced degradation of starch into sugars result in tubers that produce a dark brown product after frying. The PAIN locus (potato acid invertase) is involved in production of sugars that influence frying quality. Knockouts of PAIN alwasy keep frying quality. Non-GMO mutant alleles from PAIN that are unknown, but might be available.
The student will search our database with potato sequences for variant alleles of biologically relevant genes. This knowledge can lead to improved potato varieties.
Used skills Genetics, Bioinformatics
Requirements Two of these courses: ABG-30306 Genomics, INF-22306 Programming in Python, BIF-30806 Advanced Bioinformatics or BSc Minor Bioinformatics (WUBIF)